Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations

Abstract

Key message

A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations.

Abstract

Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0–4 QTLs in the smaller Williams 82 × PI 468916 population and 3–16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.

Communicated by Istvan Rajcan.

Stephen A. Swarm and Lianjun Sun have contributed equally to this work.

Publisher's Note

Supplementary material

Supplementary Fig. S1Discrimination of RILs into the Williams 82 × PI 468916 population (‘PI468916’) and Williams 82 × PI 479752 (‘PI479752’) based on 35,303 SNPs and five SSR markers. The first two principal components are plotted for each RIL and colored according to the k-means cluster analysis. The number of RILs classified into each group is indicated in parentheses. (PDF 600 kb)